Align Major myo-inositol transporter IolT (characterized)
to candidate BWI76_RS03110 BWI76_RS03110 MFS transporter
Query= SwissProt::O34718 (473 letters) >FitnessBrowser__Koxy:BWI76_RS03110 Length = 499 Score = 458 bits (1178), Expect = e-133 Identities = 237/461 (51%), Positives = 317/461 (68%), Gaps = 9/461 (1%) Query: 2 NKQGNQMSFLRTIILVSTFGGLLFGYDTGVLNGALPYMGEPDQLNLNAFTEGLVTSSLLF 61 N + F++ + L++T GGLLFGYDTGV++GAL +MG +L+L FT GLVTSSLLF Sbjct: 16 NSETPTTPFVKVVALIATLGGLLFGYDTGVISGALLFMGT--ELHLTPFTTGLVTSSLLF 73 Query: 62 GAALGAVFGGRMSDFNGRRKNILFLAVIFFISTIGCTFAPNVTVMIISRFVLGIAVGGAS 121 GAA GA+ G +++ GR+K IL+LAV+F I IG + AP+V MI R +LG+AVGGA+ Sbjct: 74 GAAFGALLSGNLANAAGRKKIILWLAVLFAIGAIGTSMAPDVNWMIFFRLILGVAVGGAA 133 Query: 122 VTVPAYLAEMSPVESRGRMVTQNELMIVSGQLLAFVFNAILGTTMGDNSHVWRFMLVIAS 181 TVP Y+AE++P RG++VT ELMIVSGQLLA++ NA G S WR+ML +A+ Sbjct: 134 ATVPVYIAEIAPANKRGQLVTLQELMIVSGQLLAYISNATFHEVWGGES-TWRWMLAVAT 192 Query: 182 LPALFLFFGMIRMPESPRWLVSKGRKEDALRVLKKIRDEKRAAAELQEIEFAFKKEDQLE 241 LPA+ L+FGM+ MP+SPRW KGR +A RVL++ R + EL EI ++ L Sbjct: 193 LPAVLLWFGMMFMPDSPRWYAMKGRLAEARRVLERTRHKDDVEWELLEITETLDEQRNLG 252 Query: 242 KATFKDLSVPWVRRIVFIGLGIAIVQQITGVNSIMYYGTEILRNSGFQTEAALIGNIANG 301 K F ++ PW+ ++ IG+GIA++QQ+TGVN+IMYY +L + G AAL IANG Sbjct: 253 KPRFSEIMTPWLFKLFMIGIGIAVIQQLTGVNTIMYYAPTVLTSVGMTDNAALFATIANG 312 Query: 302 VISVLATFVGIWLLGRVGRRPMLMTGLIGTTTALLLIGIFSLVL----EGSP--ALPYVV 355 V+SVL TFVGIW+LG++GRRPM M G G T L+ IG S +L G P Y+V Sbjct: 313 VVSVLMTFVGIWMLGKIGRRPMTMIGQFGCTACLVFIGAVSYLLPETVNGQPDALRAYMV 372 Query: 356 LSLTVTFLAFQQGAISPVTWLMLSEIFPLRLRGLGMGVTVFCLWMVNFAVSFTFPILLAA 415 L+ + FL+FQQGA+SPVTWL++SEIFP RLRG+ MG VF +W+ NF +S FPILLA Sbjct: 373 LAGMLLFLSFQQGALSPVTWLLMSEIFPTRLRGIFMGGAVFSMWIANFLISLFFPILLAW 432 Query: 416 IGLSTTFFIFVGLGICSVLFVKRFLPETKGLSLEQLEENFR 456 +GLS TFFIF G+G+ +FV + +PET+ SLEQ+E R Sbjct: 433 LGLSGTFFIFAGIGVFGAIFVIKCVPETRHRSLEQIEHYLR 473 Lambda K H 0.327 0.142 0.418 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 696 Number of extensions: 25 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 473 Length of database: 499 Length adjustment: 34 Effective length of query: 439 Effective length of database: 465 Effective search space: 204135 Effective search space used: 204135 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.7 bits) S2: 52 (24.6 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory